Transcriptome Meta-Analysis of Triple-Negative Breast Cancer Response to Neoadjuvant Chemotherapy

SIMPLE SUMMARY: This study aimed to identify genes associated with neoadjuvant chemotherapy (NAC) response and disease-free survival (DFS) of triple-negative breast cancer (TNBC) patients. We conducted a large-scale meta-analysis of gene expression data from multiple TNBC cohorts and analyzed four gene expression quadrants from an integrated analysis of NAC response and clinical outcomes. The study also highlighted the importance of incorporating both short-term and long-term clinical outcomes in NAC response evaluation. The findings provide insights into the complex molecular mechanisms underlying TNBC and may guide the development of personalized treatment strategies for TNBC patients. ABSTRACT: Triple-negative breast cancer (TNBC) is a heterogeneous disease with varying responses to neoadjuvant chemotherapy (NAC). The identification of biomarkers to predict NAC response and inform personalized treatment strategies is essential. In this study, we conducted large-scale gene expression meta-analyses to identify genes associated with NAC response and survival outcomes. The results showed that immune, cell cycle/mitotic, and RNA splicing-related pathways were significantly associated with favorable clinical outcomes. Furthermore, we integrated and divided the gene association results from NAC response and survival outcomes into four quadrants, which provided more insights into potential NAC response mechanisms and biomarker discovery.